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X-ray structure of human heart fatty acid-binding protein at 0.80 A resolution (holo-FABP3)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TKJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.1M Tris-HCl (pH8.5), 50% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.18 43.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.604 α = 90 b = 69.822 β = 90 c = 33.846 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2013-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.800 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 0.8 43.01 99.3 0.113 11.8 9.8 135972
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.8 0.81 0.68 2.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 0.8 24.31 129053 6847 99.29 0.12747 0.1268 0.1358 0.13993 0.1484 RANDOM 10.124
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.19 0.14 0.06
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 34.811 r_dihedral_angle_2_deg 34.503 r_sphericity_free 32.619 r_sphericity_bonded 22.242 r_dihedral_angle_4_deg 14.075 r_dihedral_angle_3_deg 12.735 r_long_range_B_refined 7.335 r_long_range_B_other 7.195 r_scbond_it 6.968 r_scbond_other 6.968
RMS Deviations Key Refinement Restraint Deviation r_rigid_bond_restr 34.811 r_dihedral_angle_2_deg 34.503 r_sphericity_free 32.619 r_sphericity_bonded 22.242 r_dihedral_angle_4_deg 14.075 r_dihedral_angle_3_deg 12.735 r_long_range_B_refined 7.335 r_long_range_B_other 7.195 r_scbond_it 6.968 r_scbond_other 6.968 r_scangle_other 6.414 r_dihedral_angle_1_deg 6.372 r_mcangle_it 2.141 r_mcangle_other 2.14 r_mcbond_it 2.004 r_mcbond_other 2.002 r_angle_refined_deg 1.982 r_angle_other_deg 0.97 r_chiral_restr 0.096 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 0.001 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1041 Nucleic Acid Atoms Solvent Atoms 242 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing